Molecular distribution within living cells is organized through multiscaled compartmentalization that enables specialized processes to occur with high efficiency. The ability to control the chemical environment at a subcellular level is limited due to deficient positional control over the aqueous stimulant. Here, a multilayered microfluidic system built from polydimethylsiloxane to separate chemical stimulants over single living cells vertically through aqueous-phase separation under laminar flow is demonstrated. Cells are cultured on top of single micrometer-scale channels inside a larger channel, allowing labeling of the apical domain of single cells through the main channel with simultaneous and distinct labeling of the basal domain via the lower microchannels. The system is transparent, which allows the use of optical microscopy to investigate the spatiotemporal response of labeled components. By employing this technique, the examination of localized subcellular domain responses in polarization, lipid bilayer mobility, and apical-to-basal signal transduction can be explored.